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| Main Authors: | , , , , |
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| Format: | Preprint |
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2024
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| Subjects: | |
| Online Access: | https://arxiv.org/abs/2411.12570 |
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| _version_ | 1866911295659311104 |
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| author | Martino, Simone Doria, Domiziano Lionello, Chiara Becchi, Matteo Pavan, Giovanni M. |
| author_facet | Martino, Simone Doria, Domiziano Lionello, Chiara Becchi, Matteo Pavan, Giovanni M. |
| contents | Reconstructing the physical complexity of many-body dynamical systems can be challenging. Starting from the trajectories of their constitutive units (raw data), typical approaches require selecting appropriate descriptors to convert them into time-series, which are then analyzed to extract interpretable information. However, identifying the most effective descriptor is often non-trivial. Here, we report a data-driven approach to compare the efficiency of various descriptors in extracting information from noisy trajectories and translating it into physically relevant insights. As a prototypical system with non-trivial internal complexity, we analyze molecular dynamics trajectories of an atomistic system where ice and water coexist in equilibrium near the solid/liquid transition temperature. We compare general and specific descriptors often used in aqueous systems: number of neighbors, molecular velocities, Smooth Overlap of Atomic Positions (SOAP), Local Environments and Neighbors Shuffling (LENS), Orientational Tetrahedral Order, and distance from the fifth neighbor ($d_5$). Using Onion Clustering -- an efficient unsupervised method for single-point time-series analysis -- we assess the maximum extractable information for each descriptor and rank them via a high-dimensional metric. Our results show that advanced descriptors like SOAP and LENS outperform classical ones due to higher signal-to-noise ratios. Nonetheless, even simple descriptors can rival or exceed advanced ones after local signal denoising. For example, $d_5$, initially among the weakest, becomes the most effective at resolving the system's non-local dynamical complexity after denoising. This work highlights the critical role of noise in information extraction from molecular trajectories and offers a data-driven approach to identify optimal descriptors for systems with characteristic internal complexity. |
| format | Preprint |
| id |
arxiv_https___arxiv_org_abs_2411_12570 |
| institution | arXiv |
| publishDate | 2024 |
| record_format | arxiv |
| spellingShingle | A data driven approach to classify descriptors based on their efficiency in translating noisy trajectories into physically-relevant information Martino, Simone Doria, Domiziano Lionello, Chiara Becchi, Matteo Pavan, Giovanni M. Materials Science Machine Learning Reconstructing the physical complexity of many-body dynamical systems can be challenging. Starting from the trajectories of their constitutive units (raw data), typical approaches require selecting appropriate descriptors to convert them into time-series, which are then analyzed to extract interpretable information. However, identifying the most effective descriptor is often non-trivial. Here, we report a data-driven approach to compare the efficiency of various descriptors in extracting information from noisy trajectories and translating it into physically relevant insights. As a prototypical system with non-trivial internal complexity, we analyze molecular dynamics trajectories of an atomistic system where ice and water coexist in equilibrium near the solid/liquid transition temperature. We compare general and specific descriptors often used in aqueous systems: number of neighbors, molecular velocities, Smooth Overlap of Atomic Positions (SOAP), Local Environments and Neighbors Shuffling (LENS), Orientational Tetrahedral Order, and distance from the fifth neighbor ($d_5$). Using Onion Clustering -- an efficient unsupervised method for single-point time-series analysis -- we assess the maximum extractable information for each descriptor and rank them via a high-dimensional metric. Our results show that advanced descriptors like SOAP and LENS outperform classical ones due to higher signal-to-noise ratios. Nonetheless, even simple descriptors can rival or exceed advanced ones after local signal denoising. For example, $d_5$, initially among the weakest, becomes the most effective at resolving the system's non-local dynamical complexity after denoising. This work highlights the critical role of noise in information extraction from molecular trajectories and offers a data-driven approach to identify optimal descriptors for systems with characteristic internal complexity. |
| title | A data driven approach to classify descriptors based on their efficiency in translating noisy trajectories into physically-relevant information |
| topic | Materials Science Machine Learning |
| url | https://arxiv.org/abs/2411.12570 |